@graphty/cytoscape-extensions 0.0.28 → 0.0.29

package/dist/lazy.d.ts.map

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package/dist/lazy.js

@@ -0,0 +1,32 @@
+/**
+ * Loading the parts of the package that are fetched on first use (the generators and datasets, the file formats, the
+ * WebGPU code), with a warning when one never arrives.
+ */
+/** How long a part may take to load before the call warns that it may never load. */
+export const STALL_MS = 5000;
+/**
+ * A part of the package loaded on first use, warning on the console when it has not loaded after STALL_MS.
+ *
+ * In a Vite 6 or 7 (Rollup) production build, the part's chunk imports the chunk that holds the consumer's entry
+ * module, because both use @graphty/graph-format and Rollup puts shared code in the chunk that loads first. When that
+ * entry module awaits the call at its top level, the entry chunk is still evaluating, so the part can never run and
+ * the await never settles. ES modules report nothing, and no package layout avoids it (the package's synchronous
+ * methods need @graphty/graph-format up front), so the warning names the cause. A slow network shows it too; the
+ * call then carries on.
+ * @param load - the dynamic import
+ * @param call - what is waiting, as the reader wrote it ("graphtyDataset")
+ * @returns the import
+ */
+export function loadPart(load, call) {
+    const timer = setTimeout(() => {
+        console.warn(`graphty: ${call} has waited ${String(STALL_MS / 1000)} s for part of @graphty/cytoscape-extensions to load. ` +
+            `If a module awaits ${call} at its top level, a Vite 6 or 7 production build never loads it: call it ` +
+            "inside an async function, or with .then(), instead. On a slow network the call carries on.");
+    }, STALL_MS);
+    const clear = () => {
+        clearTimeout(timer);
+    };
+    load.then(clear, clear);
+    return load;
+}
+//# sourceMappingURL=lazy.js.map

package/dist/lazy.js.map

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package/dist/samples.d.ts

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+/**
+ * `@graphty/cytoscape-extensions/samples`: the seeded generators and the sample datasets of @graphty/graph-samples
+ * as Cytoscape elements. cy.graphtyGenerate() and cy.graphtyDataset() load this module on their first call; every
+ * dataset downloads from graphty.app when it is asked for (no dataset's data ships in the package).
+ */
+import { type FetchDatasetOptions, type SampleGraph } from "@graphty/graph-samples";
+import * as g from "@graphty/graph-samples/generators";
+import type { ElementDefinition } from "cytoscape";
+/**
+ * Every generator by its name: the graph-samples function name in kebab case without "Graph". Each takes that
+ * function's options; the random ones take `seed` (default 0) and give the same graph for the same options on
+ * every platform.
+ */
+export declare const GENERATORS: {
+    readonly ak: typeof g.akGraph;
+    readonly "balanced-tree": typeof g.balancedTreeGraph;
+    readonly "barabasi-albert": typeof g.barabasiAlbertGraph;
+    readonly barbell: typeof g.barbellGraph;
+    readonly "bianconi-barabasi": typeof g.bianconiBarabasiGraph;
+    readonly "bipartite-configuration-model": typeof g.bipartiteConfigurationModelGraph;
+    readonly caveman: typeof g.cavemanGraph;
+    readonly "chung-lu": typeof g.chungLuGraph;
+    readonly "circular-ladder": typeof g.circularLadderGraph;
+    readonly complete: typeof g.completeGraph;
+    readonly "complete-bipartite": typeof g.completeBipartiteGraph;
+    readonly "complete-multipartite": typeof g.completeMultipartiteGraph;
+    readonly "configuration-model": typeof g.configurationModelGraph;
+    readonly "connected-caveman": typeof g.connectedCavemanGraph;
+    readonly cycle: typeof g.cycleGraph;
+    readonly "degree-corrected-sbm": typeof g.degreeCorrectedSbmGraph;
+    readonly "directed-configuration-model": typeof g.directedConfigurationModelGraph;
+    readonly "duplication-divergence": typeof g.duplicationDivergenceGraph;
+    readonly empty: typeof g.emptyGraph;
+    readonly "erdos-renyi": typeof g.erdosRenyiGraph;
+    readonly "erdos-renyi-gnm": typeof g.erdosRenyiGnmGraph;
+    readonly "forest-fire": typeof g.forestFireGraph;
+    readonly genrmf: typeof g.genrmfGraph;
+    readonly grid: typeof g.gridGraph;
+    readonly "grid-3d": typeof g.grid3dGraph;
+    readonly "grid-flow-network": typeof g.gridFlowNetwork;
+    readonly "hexagonal-lattice": typeof g.hexagonalLatticeGraph;
+    readonly hyperbolic: typeof g.hyperbolicGraph;
+    readonly hypercube: typeof g.hypercubeGraph;
+    readonly knn: typeof g.knnGraph;
+    readonly kronecker: typeof g.kroneckerGraph;
+    readonly ladder: typeof g.ladderGraph;
+    readonly "layered-flow-network": typeof g.layeredFlowNetwork;
+    readonly lfr: typeof g.lfrGraph;
+    readonly lollipop: typeof g.lollipopGraph;
+    readonly "mobius-ladder": typeof g.mobiusLadderGraph;
+    readonly named: (o: {
+        name: g.NamedGraphName;
+    } & g.WeightOptions) => SampleGraph;
+    readonly "newman-watts": typeof g.newmanWattsGraph;
+    readonly path: typeof g.pathGraph;
+    readonly petersen: typeof g.petersenGraph;
+    readonly "planted-partition": typeof g.plantedPartitionGraph;
+    readonly price: typeof g.priceGraph;
+    readonly "random-apollonian": typeof g.randomApollonianGraph;
+    readonly "random-bipartite": typeof g.randomBipartiteGraph;
+    readonly "random-dag": typeof g.randomDagGraph;
+    readonly "random-geometric": typeof g.randomGeometricGraph;
+    readonly "random-order-dag": typeof g.randomOrderDagGraph;
+    readonly "random-recursive-tree": typeof g.randomRecursiveTreeGraph;
+    readonly "random-regular": typeof g.randomRegularGraph;
+    readonly "random-tree": typeof g.randomTreeGraph;
+    readonly "ring-of-cliques": typeof g.ringOfCliquesGraph;
+    readonly rmat: typeof g.rmatGraph;
+    readonly star: typeof g.starGraph;
+    readonly "stochastic-block-model": typeof g.stochasticBlockModelGraph;
+    readonly "triangular-lattice": typeof g.triangularLatticeGraph;
+    readonly "watts-strogatz": typeof g.wattsStrogatzGraph;
+    readonly waxman: typeof g.waxmanGraph;
+    readonly wheel: typeof g.wheelGraph;
+    readonly "wilson-maze": typeof g.wilsonMazeGraph;
+};
+/** A generator name. */
+export type GeneratorName = keyof typeof GENERATORS;
+/** The graphs the "named" generator knows, for `graphtyGenerate("named", { name })`. */
+export { NAMED_GRAPH_NAMES } from "@graphty/graph-samples/generators";
+/** The options of a generator. */
+export type GeneratorOptions<N extends GeneratorName> = Parameters<(typeof GENERATORS)[N]>[0];
+/**
+ * The small datasets, which the package used to bundle. Every dataset now downloads from graphty.app like the rest.
+ * @deprecated every dataset is downloaded; graph-samples' `DATASET_NAMES` lists them all
+ */
+export declare const BUNDLED_DATASET_NAMES: readonly string[];
+/** A generated graph or a dataset as Cytoscape element definitions. */
+export interface SampleElements {
+    /** The nodes, then the edges. Node ids are the dataset's names, or "0", "1", ... for a generated graph. */
+    readonly elements: ElementDefinition[];
+    /** Whether the graph is directed: pass it as `directed` to the algorithms. */
+    readonly directed: boolean;
+}
+/**
+ * Generates a graph. Ground-truth columns (`community`, `side`, `layer`, ...) become node data fields; weights
+ * become `data.weight`; coordinates (`x` and `y`) become node positions. Edge k gets the id "e<k>", so the same
+ * options and seed give the same element ids as well as the same graph.
+ * @param name - the generator
+ * @param options - the generator's options
+ * @returns the elements and the direction
+ * @throws RangeError for an unknown generator name, or an option the generator does not take
+ */
+export declare function generateElements<N extends GeneratorName>(name: N, options: GeneratorOptions<N>): SampleElements;
+/**
+ * Loads a sample dataset from graphty.app (see graph-samples' `DATASETS` for the list, with each one's source,
+ * citation and license). A drawn dataset's saved `x` and `y` become node positions, placed where Cytoscape drew them.
+ * @param name - the dataset name, e.g. "karate"
+ * @param options - the base URL (a mirror of your own), the fetch implementation and an abort signal
+ * @returns the elements and the direction
+ * @throws the signal's reason (an AbortError) when it is aborted before the dataset is decoded
+ * @throws RangeError for a name that is not a known dataset, unless `baseUrl` is given
+ */
+export declare function datasetElements(name: string, options?: FetchDatasetOptions): Promise<SampleElements>;
+//# sourceMappingURL=samples.d.ts.map

package/dist/samples.d.ts.map

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package/dist/samples.js

@@ -0,0 +1,237 @@
+/**
+ * `@graphty/cytoscape-extensions/samples`: the seeded generators and the sample datasets of @graphty/graph-samples
+ * as Cytoscape elements. cy.graphtyGenerate() and cy.graphtyDataset() load this module on their first call; every
+ * dataset downloads from graphty.app when it is asked for (no dataset's data ships in the package).
+ */
+import { fromEdgeArrays } from "@graphty/graph-format";
+import { DATASET_NAMES, fetchDataset } from "@graphty/graph-samples";
+import * as g from "@graphty/graph-samples/generators";
+import { GENERATOR_OPTION_NAMES } from "./algorithm-options.js";
+import { flipY, snapshotToElements } from "./elements.js";
+/**
+ * Every generator by its name: the graph-samples function name in kebab case without "Graph". Each takes that
+ * function's options; the random ones take `seed` (default 0) and give the same graph for the same options on
+ * every platform.
+ */
+export const GENERATORS = {
+    ak: g.akGraph,
+    "balanced-tree": g.balancedTreeGraph,
+    "barabasi-albert": g.barabasiAlbertGraph,
+    barbell: g.barbellGraph,
+    "bianconi-barabasi": g.bianconiBarabasiGraph,
+    "bipartite-configuration-model": g.bipartiteConfigurationModelGraph,
+    caveman: g.cavemanGraph,
+    "chung-lu": g.chungLuGraph,
+    "circular-ladder": g.circularLadderGraph,
+    complete: g.completeGraph,
+    "complete-bipartite": g.completeBipartiteGraph,
+    "complete-multipartite": g.completeMultipartiteGraph,
+    "configuration-model": g.configurationModelGraph,
+    "connected-caveman": g.connectedCavemanGraph,
+    cycle: g.cycleGraph,
+    "degree-corrected-sbm": g.degreeCorrectedSbmGraph,
+    "directed-configuration-model": g.directedConfigurationModelGraph,
+    "duplication-divergence": g.duplicationDivergenceGraph,
+    empty: g.emptyGraph,
+    "erdos-renyi": g.erdosRenyiGraph,
+    "erdos-renyi-gnm": g.erdosRenyiGnmGraph,
+    "forest-fire": g.forestFireGraph,
+    genrmf: g.genrmfGraph,
+    grid: g.gridGraph,
+    "grid-3d": g.grid3dGraph,
+    "grid-flow-network": g.gridFlowNetwork,
+    "hexagonal-lattice": g.hexagonalLatticeGraph,
+    hyperbolic: g.hyperbolicGraph,
+    hypercube: g.hypercubeGraph,
+    knn: g.knnGraph,
+    kronecker: g.kroneckerGraph,
+    ladder: g.ladderGraph,
+    "layered-flow-network": g.layeredFlowNetwork,
+    lfr: g.lfrGraph,
+    lollipop: g.lollipopGraph,
+    "mobius-ladder": g.mobiusLadderGraph,
+    named: (o) => {
+        // checked here: graph-samples' own error points at a list this package's readers cannot see
+        if (!g.NAMED_GRAPH_NAMES.includes(o.name)) {
+            throw unknownName("named graph", o.name, g.NAMED_GRAPH_NAMES);
+        }
+        return g.namedGraph(o.name, o);
+    },
+    "newman-watts": g.newmanWattsGraph,
+    path: g.pathGraph,
+    petersen: g.petersenGraph,
+    "planted-partition": g.plantedPartitionGraph,
+    price: g.priceGraph,
+    "random-apollonian": g.randomApollonianGraph,
+    "random-bipartite": g.randomBipartiteGraph,
+    "random-dag": g.randomDagGraph,
+    "random-geometric": g.randomGeometricGraph,
+    "random-order-dag": g.randomOrderDagGraph,
+    "random-recursive-tree": g.randomRecursiveTreeGraph,
+    "random-regular": g.randomRegularGraph,
+    "random-tree": g.randomTreeGraph,
+    "ring-of-cliques": g.ringOfCliquesGraph,
+    rmat: g.rmatGraph,
+    star: g.starGraph,
+    "stochastic-block-model": g.stochasticBlockModelGraph,
+    "triangular-lattice": g.triangularLatticeGraph,
+    "watts-strogatz": g.wattsStrogatzGraph,
+    waxman: g.waxmanGraph,
+    wheel: g.wheelGraph,
+    "wilson-maze": g.wilsonMazeGraph,
+};
+/** The graphs the "named" generator knows, for `graphtyGenerate("named", { name })`. */
+export { NAMED_GRAPH_NAMES } from "@graphty/graph-samples/generators";
+/**
+ * The small datasets, which the package used to bundle. Every dataset now downloads from graphty.app like the rest.
+ * @deprecated every dataset is downloaded; graph-samples' `DATASET_NAMES` lists them all
+ */
+export const BUNDLED_DATASET_NAMES = [
+    "karate",
+    "florentine-families",
+    "davis-southern-women",
+    "les-miserables",
+    "football",
+    "political-books",
+    "dolphins",
+    "contiguous-usa",
+    "knuth-miles",
+    "celegans-neural",
+    "political-blogs",
+    "openflights",
+    "yeast-perturbation",
+    "stelzl-interactome",
+    "wikipathways-senescence-autophagy",
+    "go-slim-generic",
+];
+/**
+ * The number of single-character edits that turn one string into the other.
+ * @param a - one string
+ * @param b - the other
+ * @returns the Levenshtein distance
+ */
+function editDistance(a, b) {
+    let prev = Array.from({ length: b.length + 1 }, (_, j) => j);
+    for (let i = 1; i <= a.length; i++) {
+        const row = [i];
+        for (let j = 1; j <= b.length; j++) {
+            row[j] = Math.min(prev[j] + 1, row[j - 1] + 1, prev[j - 1] + (a[i - 1] === b[j - 1] ? 0 : 1));
+        }
+        prev = row;
+    }
+    return prev[b.length];
+}
+/**
+ * The error for an unknown name, naming the closest known one when one is close and listing them all.
+ * @param kind - what the name names ("dataset", "generator", "named graph")
+ * @param name - the unknown name
+ * @param names - the known names
+ * @returns a RangeError
+ */
+function unknownName(kind, name, names) {
+    let best = "";
+    let bestDistance = Infinity;
+    for (const known of names) {
+        const d = editDistance(name, known);
+        if (d < bestDistance) {
+            best = known;
+            bestDistance = d;
+        }
+    }
+    const hint = bestDistance <= Math.max(2, name.length / 3) ? ` (did you mean ${JSON.stringify(best)}?)` : "";
+    return new RangeError(`unknown ${kind} ${JSON.stringify(name)}${hint}; the ${kind}s are ${names.join(", ")}`);
+}
+/**
+ * The elements of a graph-samples graph.
+ * @param graph - the graph
+ * @returns the elements and the direction
+ */
+function fromSample(graph) {
+    const snapshot = "src" in graph ? fromEdgeArrays(graph) : graph;
+    return { elements: snapshotToElements(snapshot), directed: snapshot.directed };
+}
+/**
+ * A generated graph with its coordinate columns `x` and `y` (the lattices with `positions: true`, and the geometric
+ * generators) as one position column, so they become node positions; `z` stays a data field.
+ * @param graph - the generated graph
+ * @returns the graph, its x and y as a position
+ */
+function withPosition(graph) {
+    const { x, y, ...rest } = graph.nodeColumns ?? {};
+    if (!ArrayBuffer.isView(x) || !ArrayBuffer.isView(y)) {
+        return graph;
+    }
+    const xs = x;
+    const ys = y;
+    const xy = new Float64Array(2 * graph.nodeCount);
+    for (let i = 0; i < graph.nodeCount; i++) {
+        xy[2 * i] = xs[i];
+        xy[2 * i + 1] = ys[i];
+    }
+    return {
+        ...graph,
+        nodeColumns: { ...rest, position: { data: xy, decl: { dtype: "f64", components: 2, role: "position" } } },
+    };
+}
+/**
+ * Generates a graph. Ground-truth columns (`community`, `side`, `layer`, ...) become node data fields; weights
+ * become `data.weight`; coordinates (`x` and `y`) become node positions. Edge k gets the id "e<k>", so the same
+ * options and seed give the same element ids as well as the same graph.
+ * @param name - the generator
+ * @param options - the generator's options
+ * @returns the elements and the direction
+ * @throws RangeError for an unknown generator name, or an option the generator does not take
+ */
+export function generateElements(name, options) {
+    const make = GENERATORS[name];
+    if (make === undefined) {
+        throw unknownName("generator", name, Object.keys(GENERATORS));
+    }
+    // a misspelled option (seeed, position) would otherwise run with the default and give a plausible graph
+    const known = GENERATOR_OPTION_NAMES[name] ?? [];
+    for (const [k, v] of Object.entries(options ?? {})) {
+        if (v !== undefined && !known.includes(k)) {
+            throw new RangeError(`generator ${JSON.stringify(name)}: unknown option ${k}; the options are ${known.join(", ")}`);
+        }
+    }
+    const r = fromSample(withPosition(make(options)));
+    let k = 0;
+    for (const el of r.elements) {
+        // node ids are "0", "1", ..., so "e<k>" never collides with one
+        if (el.group === "edges") {
+            el.data.id = `e${String(k++)}`;
+        }
+    }
+    return r;
+}
+/**
+ * Loads a sample dataset from graphty.app (see graph-samples' `DATASETS` for the list, with each one's source,
+ * citation and license). A drawn dataset's saved `x` and `y` become node positions, placed where Cytoscape drew them.
+ * @param name - the dataset name, e.g. "karate"
+ * @param options - the base URL (a mirror of your own), the fetch implementation and an abort signal
+ * @returns the elements and the direction
+ * @throws the signal's reason (an AbortError) when it is aborted before the dataset is decoded
+ * @throws RangeError for a name that is not a known dataset, unless `baseUrl` is given
+ */
+export async function datasetElements(name, options = {}) {
+    // checked here too, not only by fetch: a custom fetch may ignore the signal
+    options.signal?.throwIfAborted();
+    // only graphty.app's own list is checked: a custom baseUrl may serve any name
+    if (options.baseUrl === undefined && !DATASET_NAMES.includes(name)) {
+        throw unknownName("dataset", name, DATASET_NAMES);
+    }
+    const graph = await fetchDataset(name, options);
+    options.signal?.throwIfAborted();
+    const r = fromSample(graph);
+    // a drawn dataset's saved x and y (y growing upward) become the position Cytoscape drew (y growing downward)
+    for (const el of r.elements) {
+        const { x, y } = el.data;
+        if (typeof x === "number" && typeof y === "number") {
+            el.position = { x, y: flipY(y) };
+            delete el.data.x;
+            delete el.data.y;
+        }
+    }
+    return r;
+}
+//# sourceMappingURL=samples.js.map

package/dist/samples.js.map

@@ -0,0 +1 @@
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package/dist/snapshot.d.ts

@@ -0,0 +1,81 @@
+/**
+ * Conversion between Cytoscape elements and the graph-format snapshot every graphty layout and algorithm takes.
+ *
+ * A snapshot addresses nodes and edges by dense index. Here node index i is `nodes[i]` and edge index e is
+ * `edges[e]`, in the collection order Cytoscape gave, so a result array maps back to elements by position.
+ */
+import { type GraphSnapshot } from "@graphty/graph-format";
+import type { Collection, Core, EdgeCollection, EdgeSingular, NodeCollection } from "cytoscape";
+/** How to read a Cytoscape collection as a graph. */
+export interface SnapshotOptions {
+    /** Build a directed snapshot. Default false. */
+    readonly directed?: boolean | undefined;
+    /**
+     * The edge weight: an edge data field (a missing or non-numeric value counts as 1), or a function of the edge
+     * as Cytoscape's built-in algorithms take it. Default: unweighted. A function result is not cached.
+     */
+    readonly weight?: string | ((edge: EdgeSingular) => number) | undefined;
+}
+/** A node set given the Cytoscape way: a selector over the collection's nodes, or a collection. */
+export type NodeSelection = string | Collection | NodeCollection;
+/** A snapshot of a Cytoscape collection plus the element arrays its indices refer to. */
+export interface CytoscapeSnapshot {
+    readonly snapshot: GraphSnapshot;
+    /** Node index i is `nodes[i]`. */
+    readonly nodes: NodeCollection;
+    /** Edge index e is `edges[e]`: the collection's edges whose two endpoints are both in `nodes`. */
+    readonly edges: EdgeCollection;
+}
+/**
+ * The core of a collection. Every collection has `cy()` at run time; Cytoscape's typings declare it only on single
+ * elements.
+ * @param eles - the collection
+ * @returns its core
+ */
+export declare function coreOf(eles: Collection | NodeCollection | EdgeCollection): Core;
+/**
+ * Keeps a snapshot from being released while a run uses it: when the cache drops it (a data change, say) during
+ * the run, its release waits until every hold on it is let go.
+ * @param s - the snapshot
+ * @returns lets go of the hold; calling it again does nothing
+ */
+export declare function hold(s: GraphSnapshot): () => void;
+/**
+ * Subscribes to the snapshots a core's cache lets go of.
+ * @param cy - the core
+ * @param listener - called with the dropped snapshots
+ * @returns the unsubscriber
+ */
+export declare function onSnapshotsDropped(cy: Core, listener: (dropped: readonly GraphSnapshot[]) => void): () => void;
+/**
+ * Builds (or returns the cached) snapshot of a collection. The cache holds one snapshot per option set per core and
+ * is dropped when an element is added, removed, moved to other endpoints, or has its data changed.
+ * @param eles - the collection to read: its nodes, and its edges whose endpoints are both in it
+ * @param options - directed flag and weight field
+ * @returns the snapshot and the element arrays its indices refer to
+ */
+export declare function toSnapshot(eles: Collection | NodeCollection | EdgeCollection, options?: SnapshotOptions): CytoscapeSnapshot;
+/**
+ * Writes one value per element into its data, in one batch (one style pass).
+ * @param elements - `nodes` or `edges` of a CytoscapeSnapshot, in index order
+ * @param values - one value per element
+ * @param field - the data field to write
+ */
+export declare function writeData(elements: NodeCollection | EdgeCollection, values: ArrayLike<number>, field: string): void;
+/**
+ * Indices of the snapshot's nodes in a selection.
+ * @param cs - the snapshot
+ * @param sel - a selector or a collection
+ * @returns the node indices, in collection order
+ */
+export declare function indicesOf(cs: CytoscapeSnapshot, sel: NodeSelection): number[];
+/**
+ * The index of the first node of a selection.
+ * @param cs - the snapshot
+ * @param sel - a selector or a collection, or undefined
+ * @param what - the option name, for the error
+ * @returns the index, or undefined when no selection was given
+ * @throws Error when the selection matches no node of the snapshot
+ */
+export declare function indexOf(cs: CytoscapeSnapshot, sel: NodeSelection | undefined, what: string): number | undefined;
+//# sourceMappingURL=snapshot.d.ts.map

package/dist/snapshot.d.ts.map

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